Keeping up with the genomes: efficient learning of our increasing knowledge of the tree of life
Abstract Background It is a computational challenge for current metagenomic classifiers to keep up with the pace of training data generated from genome sequencing projects, such as the exponentially-growing NCBI RefSeq bacterial genome database. When new reference sequences are added to training dat...
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| Format: | Article |
| Language: | English |
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BMC
2020-09-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-020-03744-7 |
| _version_ | 1818995204132175872 |
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| author | Zhengqiao Zhao Alexandru Cristian Gail Rosen |
| author_facet | Zhengqiao Zhao Alexandru Cristian Gail Rosen |
| author_sort | Zhengqiao Zhao |
| collection | DOAJ |
| description | Abstract Background It is a computational challenge for current metagenomic classifiers to keep up with the pace of training data generated from genome sequencing projects, such as the exponentially-growing NCBI RefSeq bacterial genome database. When new reference sequences are added to training data, statically trained classifiers must be rerun on all data, resulting in a highly inefficient process. The rich literature of “incremental learning” addresses the need to update an existing classifier to accommodate new data without sacrificing much accuracy compared to retraining the classifier with all data. Results We demonstrate how classification improves over time by incrementally training a classifier on progressive RefSeq snapshots and testing it on: (a) all known current genomes (as a ground truth set) and (b) a real experimental metagenomic gut sample. We demonstrate that as a classifier model’s knowledge of genomes grows, classification accuracy increases. The proof-of-concept naïve Bayes implementation, when updated yearly, now runs in 1/4 t h of the non-incremental time with no accuracy loss. Conclusions It is evident that classification improves by having the most current knowledge at its disposal. Therefore, it is of utmost importance to make classifiers computationally tractable to keep up with the data deluge. The incremental learning classifier can be efficiently updated without the cost of reprocessing nor the access to the existing database and therefore save storage as well as computation resources. |
| first_indexed | 2024-12-20T21:10:07Z |
| format | Article |
| id | doaj.art-e847785e00c340b587bc1bd2e52b027b |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-20T21:10:07Z |
| publishDate | 2020-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-e847785e00c340b587bc1bd2e52b027b2022-12-21T19:26:33ZengBMCBMC Bioinformatics1471-21052020-09-0121112310.1186/s12859-020-03744-7Keeping up with the genomes: efficient learning of our increasing knowledge of the tree of lifeZhengqiao Zhao0Alexandru Cristian1Gail Rosen2Ecological and Evolutionary Signal-process and Informatics (EESI) Lab, Department of Electrical and Computer Engineering, Drexel UniversityDepartment of Computer Science, Drexel UniversityEcological and Evolutionary Signal-process and Informatics (EESI) Lab, Department of Electrical and Computer Engineering, Drexel UniversityAbstract Background It is a computational challenge for current metagenomic classifiers to keep up with the pace of training data generated from genome sequencing projects, such as the exponentially-growing NCBI RefSeq bacterial genome database. When new reference sequences are added to training data, statically trained classifiers must be rerun on all data, resulting in a highly inefficient process. The rich literature of “incremental learning” addresses the need to update an existing classifier to accommodate new data without sacrificing much accuracy compared to retraining the classifier with all data. Results We demonstrate how classification improves over time by incrementally training a classifier on progressive RefSeq snapshots and testing it on: (a) all known current genomes (as a ground truth set) and (b) a real experimental metagenomic gut sample. We demonstrate that as a classifier model’s knowledge of genomes grows, classification accuracy increases. The proof-of-concept naïve Bayes implementation, when updated yearly, now runs in 1/4 t h of the non-incremental time with no accuracy loss. Conclusions It is evident that classification improves by having the most current knowledge at its disposal. Therefore, it is of utmost importance to make classifiers computationally tractable to keep up with the data deluge. The incremental learning classifier can be efficiently updated without the cost of reprocessing nor the access to the existing database and therefore save storage as well as computation resources.http://link.springer.com/article/10.1186/s12859-020-03744-7Incremental learningNaïve Bayes taxanomic classifierRefSeqMetagenomics |
| spellingShingle | Zhengqiao Zhao Alexandru Cristian Gail Rosen Keeping up with the genomes: efficient learning of our increasing knowledge of the tree of life BMC Bioinformatics Incremental learning Naïve Bayes taxanomic classifier RefSeq Metagenomics |
| title | Keeping up with the genomes: efficient learning of our increasing knowledge of the tree of life |
| title_full | Keeping up with the genomes: efficient learning of our increasing knowledge of the tree of life |
| title_fullStr | Keeping up with the genomes: efficient learning of our increasing knowledge of the tree of life |
| title_full_unstemmed | Keeping up with the genomes: efficient learning of our increasing knowledge of the tree of life |
| title_short | Keeping up with the genomes: efficient learning of our increasing knowledge of the tree of life |
| title_sort | keeping up with the genomes efficient learning of our increasing knowledge of the tree of life |
| topic | Incremental learning Naïve Bayes taxanomic classifier RefSeq Metagenomics |
| url | http://link.springer.com/article/10.1186/s12859-020-03744-7 |
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